Open Microscopy Environment

Hi there,
soon we will start cell culture experimenting where one chamber may have treatments (which become tags) A,B and C, the second A,B and D and the tenth could have E,F and G. Thus each chamber has a unique combination of treatments (therefore unique set of tags) but may share some of them with others. We will be taking loads of pictures running our microscope with Matlab scripts. Ideally we would like to use some scripts so that the images would be imported automatically into Omero, and/or more importantly automatic tagging, since it will probably be quite a work to manually pick the pictures for previously described tagging. I tried working a bit with the OmeroMatlab toolbox with no luck so far and frankly it doesn't seem to support what we want to do. Has anyone done anything similar? Do you think this is possible to perform?

Thanks,
Jon

Hi Jon,

your best bet will probably be to write your own importer using the ImportLibrary class if you would like to control everything from within Matlab. Another option would be to launch the CLI importer from matlab and then capture the stdout which contains the newly created pixel ids for annotation. If the examples pointed to under "ImportLibrary" don't help, let us know and we'll find some more.

Cheers,
~Josh.

Thanks for the help,
I think, however, that we'll just implement the tagging through file naming instead. Seems simpler and less time consuming. I tried out a few aspects of the Omero Insight advanced search feature and very fortunately it searches for whole words, meaning that if you have three pictures called Test_ABC, Test_A_B_C, Test _A and search for "A" you will only find the latter two pictures. This solves the more important problem without needing to create super long file names.

Jon